Table 5.

Antimicrobial susceptibility and resistance genes and IS elements for the six MDR B. fragilis strains

Identified genes are displayed next to the relevant antimicrobials. Identified IS elements in correct orientation (opposite strand) directly upstream of the genes are included. The % ID and % COV refer to the gene hit. Hits with % ID or % COV <98% were confirmed with blastx searches. The hits for ugd represent possible homologues for genes encoding PmrE, which is involved in polymyxin resistance in Gram-negative bacteria. Full ABRicate results with nucleotide positions and information on the IS elements are available in Table S4.

Antimicrobial susceptibility*				AMR genes and IS elements
Strain	Antimi-crobial	Etest MIC (mg l− 1)	Result	Gene	Upstream IS element	Sequence†	% ID	% COV	Associated resistance to drug class
BFO17	MEM	>32	R	cfiA11	IS614B	Chr	100.00	99.20	Carbapenem
	IPM	>32	R
	MTZ	>32	R	nimJ	IS614B	Chr	99.40	100.00	Nitroimidazole
				nimJ	IS614B	Chrc	99.40	100.00	Nitroimidazole
	CLI	0.094	S
	TZP	>256	R
				tetQ		Chr	99.34	99.34	Tetracycline
				cfxA4		Chr	85.71	100.00	Cephamycin
				bexB		Chrc	91.21	100.00	Fluoroquinolone
				bexA		Chr	73.77	99.02	Fluoroquinolone
BFO18	MEM	>32	R	cfiA2_1	ISBf12	Chr	100.00	100.00	Carbapenem
	IPM	16	R				100.00	100.00
	MTZ	16	R	nimD	IS1169	S	99.19	100.00	Nitroimidazole
	CLI	6	R	ermF‡	IS4351	Chrc	99.83	72.03	Clindamycin
					ISBthe1‡	Chrc	70.97	97.19
				erm(F)§		Chrc	99.58	29.71
				lnu(AN2)		Chrc	100.00	100.00	Clindamycin
	TZP	>256	R
				ugd		Chr	65.69	53.04	Polymyxin
				bexA		Chrc	73.60	99.02	Fluoroquinolone
				bexB		Chr	91.14	100.00	Fluoroquinolone
				tet(Q)		Chrc	99.79	100.00	Tetracycline
				mef(En2)		Chrc	99.83	100.00	Macrolides
S01	MEM	>32	R	cfiA13_1	IS1187	Chr	99.20	100.00	Carbapenem
	IPM	16	R
	MTZ	64	R	nimE	ISBf6	pBFS01_2	100.00	100.00	Nitroimidazole
	CLI	>32	R	erm(F)	IS1187	Chr	99.50	100.00	Clindamycin
	TZP	6	S
				tetQ		Chr	90.02	99.95	Tetracycline
				tet(Q)		Chrc	99.84	100.00	Tetracycline
				bexB		Chrc	91.06	100.00	Fluoroquinolone
				bexA		Chr	74.03	98.80	Fluoroquinolone
BFO42	MEM	0.094	S
	IPM	0.25	S
	MTZ	8	R	nimA	ISBf13	pBFO32_1	98.64	96.61	Nitroimidazole
	CLI	>256	R	erm(F)	IS613	Chr	99.50	100.00	Clindamycin
				lnu(AN2)		Chr	100.00	100.00	Clindamycin
	TZP	0.38	S
				ugd		Chr	70.38	31.45	Polymyxin
				cepA-49		Chrc	100.00	100.00	Cephalosporin
				mef(En2)		Chr	99.83	100.00	Macrolide
				ugd		Chr	71.15	31.11	Polymyxin
				tetQ		Chrc	100.00	100.00	Tetracycline
				bexB		Chr	99.12	100.00	Fluoroquinolone
				ere(D)		Chr	96.66	100.00	Erythromycin
				aadS		Chrc	99.88	100.00	Aminoglycoside
				OXA-347	IS613	Chrc	100.00	100.00	Penicillin, cephalosporin
				bexA		Chr	75.09	99.62	Fluoroquinolone
BFO67	MEM	8	R	cfiA13_1	None	Chr	100.00	100.00	Carbapenem
	IPM	0.5	S
	MTZ	0.19	S
	CLI	0.38	S
	TZP	2	S
				cfxA2	ISBf11	Chr	99.69	100.00	Cephamycin
				mef(En2)		Chr	99.75	100.00	Macrolide
				lnu(AN2)		Chr	100.00	100.00	Clindamycin
				ugd		Chrc	66.76	56.30	Polymyxin
				tet(Q)		Chr	100.00	100.00	Tetracycline
				bexB		Chrc	90.92	100.00	Fluoroquinolone
				bexA		Chr	73.90	99.02	Fluoroquinolone
BFO65	MEM	32	R	cfiA2_1	None	Chr	100.00	100.00	Carbapenem
	IPM	1	S
	MTZ	0.25	S
	CLI	>256	R	ermB		Chrc	99.19	98.66	Clindamycin
	TZP	2	S
				ugd		Chr	69.84	31.45	Polymyxin
				tetQ		Chrc	90.02	99.95	Tetracycline
				aadE		Chrc	100.00	100.00	Aminoglycoside
				aad9		Chrc	100.00	100.00	Aminoglycoside
				bexB		Chrc	90.92	100.00	Fluoroquinolone
				bexA		Chr	73.53	99.02	Fluoroquinolone
				cfxA2	IS614	Chrc	100.00	100.00	Cephamycin
				tet(Q)		Chrc	99.84	100.00	Tetracycline

Chr, Chromosome; MEM, meropenem; IPM, imipenem; MTZ, metronidazole; CLI, clindamycin; TZP, piperacillin/tazobactam.

*Results from previously published work following EUCAST (European Committee on Antimicrobial Susceptibility Testing) breakpoints [14].

†A subscript letter C denotes the complement strand.

‡A transposase has inserted itself, splitting the ermF gene in two.